I am totally lost as to how to merge some vcf files. The problem is they are vcf.gz.tbi files (of individual patients) and I cannot figure out how to unindex them before unzipping them so that I can merge them (so that I can do an association study later)
I have installed vcf tools and tabix but everything I can find on line is to do with creation of .tbi files using these, and not the reverse.
Anyone know what to do? (Please be gentle with the lingo, I am very new to this)
Thanks
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HumeMarx •
You can ignore the tbi files, they're just an index (yes, like the index at the end of a book) and aren't the actual files you want to merge. The files you actually want to merge end either in vcf.gz or vcf (or something like that).
Thanks.
Is vcf.gz.vcfidx also an indexed file?
Because they seem to be the only two type of files my data comes in.
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HumeMarx •
That's likely also an index (from vcftools, rather than tabix). Your actual data is elsewhere, perhaps on a remote server. You should ask whomever provided you with this data.
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Devon Ryan
Thank you very much. It saves me from crashing the terminal a couple of times.
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HumeMarx •
On a semi-related note: if I'd like to convert from the vcf format to plink bed/bim/fam, is the .tbi file at all necessary?
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